A story: unpaired adenosine bases in ribosomal RNAs

In 1985 an analysis of the Escherichia coli 16 S rRNA covariation-based structure model revealed a strong bias for unpaired adenosines. The same analysis revealed that the majority of the G, C, and U bases were paired. These biases are (now) consistent with the high percentage of unpaired adenosine nucleotides in several structure motifs. An analysis of a larger set of bacterial comparative 16 S and 23 S rRNA structure models has substantiated this initial finding and revealed new biases in the distribution of adenosine nucleotides in loop regions. The majority of the adenosine nucleotides are unpaired, while the majority of the G, C, and U bases are paired in the covariation-based structure model. The unpaired adenosine nucleotides predominate in the middle and at the 3′ end of loops, and are the second most frequent nucleotide type at the 5′ end of loops (G is the most common nucleotide). There are additional biases for unpaired adenosine nucleotides at the 3′ end of loops and adjacent to a G at the 5’ end of the helix. The most prevalent consecutive nucleotides are GG, GA, AG, and AA. A total of 70% of the GG sequences are within helices, while more than 70% of the AA sequences are unpaired. Nearly 50% of the GA sequences are unpaired, and approximately one-third of the AG sequences are within helices while another third are at the 3′ loop.5′ helix junction. Unpaired positions with an adenosine nucleotide in more than 50% of the sequences at the 3′ end of 16 S and 23 S rRNA loops were identified and arranged into the A-motif categories XA Z, AA Z, XA G, AA G, and AA G: U, where G or Z is paired, G: U is a base-pair, and X is not an A and Z is not a G in more than 50% of the sequences. These sequence motifs were associated with several structural motifs, such as adenosine platforms, E and E-like loops, A: A and A: G pairings at the end of helices, G: A tandem base-pairs, GNRA tetraloop hairpins, and U-turns.